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Cayrou C.,French National Center for Scientific Research | Ballester B.,French Institute of Health and Medical Research | Ballester B.,Aix - Marseille University | Peiffer I.,French National Center for Scientific Research | And 7 more authors.
Genome Research | Year: 2015

To unveil the still-elusive nature of metazoan replication origins, we identified them genome-wide and at unprecedented high-resolution in mouse ES cells. This allowed initiation sites (IS) and initiation zones (IZ) to be differentiated. We then characterized their genetic signatures and organization and integrated these data with 43 chromatin marks and factors. Our results reveal that replication origins can be grouped into three main classes with distinct organization, chromatin environment, and sequence motifs. Class 1 contains relatively isolated, low-efficiency origins that are poor in epigenetic marks and are enriched in an asymmetric AC repeat at the initiation site. Late origins are mainly found in this class. Class 2 origins are particularly rich in enhancer elements. Class 3 origins are the most efficient and are associated with open chromatin and polycomb protein-enriched regions. The presence of Origin G-rich Repeated elements (OGRE) potentially forming G-quadruplexes (G4) was confirmed at most origins. These coincide with nucleosome-depleted regions located upstream of the initiation sites, which are associated with a labile nucleosome containing H3K64ac. These data demonstrate that specific chromatin landscapes and combinations of specific signatures regulate origin localization. They explain the frequently observed links between DNA replication and transcription. They also emphasize the plasticity of metazoan replication origins and suggest that in multicellular eukaryotes, the combination of distinct genetic features and chromatin configurations act in synergy to define and adapt the origin profile. © 2015 Robin et al.

Brisson L.,French Institute of Health and Medical Research | Brisson L.,Institute Paoli Calmettes | Brisson L.,Aix - Marseille University | Brisson L.,French National Center for Scientific Research | And 26 more authors.
Cell Reports | Year: 2015

In cancer, immune cells can play conflicting roles, either protective, by elimination of tumor cells during immune surveillance, or detrimental, by promoting carcinogenesis during inflammation. We report here that the thymus-specific serine protease (TSSP), which is involved in CD4+ Tcell maturation in the thymus, exerts a tumor suppressor activity. Mice genetically deficient for TSSP are highly prone to spontaneous cancer development. The absence of TSSP also increases the rate of induced colitis-associated colorectal (CAC) tumor formation, through exacerbated colon inflammation. Adoptive transfer of Tcells in various combinations (CD4+ and CD8+ from wild-type and/or knockout mice) into Tcell-deficient mice showed that the TSSP-deficient CD4+ Tcell compartment promotes tumor development, associated with high levels of the cytokine IL-17A. Inhibition of IL-17A during CAC tumor formation prevents the increased carcinogenesis and colic immune disequilibrium observed in TSSP-deficient mice. Therefore, our data demonstrate that antitumoral immune surveillance requires thymic TSSP-driven production of CD4+ Tcells contributing to inflammatory balance. © 2015 The Authors.

Serge A.,Aix - Marseille University | Bailly A.-L.,Aix - Marseille University | Aurrand-Lions M.,Aix - Marseille University | Imhof B.A.,University of Geneva | And 2 more authors.
Journal of Immunological Methods | Year: 2015

To decipher the complex topology of lymphoid structures, we developed an automated process called Full Organ Reconstruction in 3D (For3D). A dedicated image-processing pipeline is applied to entire collections of immunolabeled serial sections, acquired with a slide-scanning microscope. This method is automated, flexible and readily applicable in two days to frozen or paraffin-embedded organs stained by fluorescence or brightfield immunohistochemistry. 3D-reconstructed organs can be visualized, rotated and analyzed to quantify substructures of interest. Usefulness of For3D is exemplified here through topological analysis of several mouse lymphoid organs exhibiting a complex organization: (i) the thymus, composed of two compartments, a medulla intricately imbricated into a surrounding cortex, (ii) lymph nodes, also highly compartmentalized into cortex, paracortex and medulla and (iii) the vascularization of an EG7 primary thymoma. This open-source algorithm, based on ImageJ and Matlab scripts, offers a user-friendly interface and is widely applicable to any organ or tissue, hence readily adaptable to a broad range of biomedical samples. © 2015 Elsevier B.V.

Pekowska A.,Center Dimmunologie Of Marseille Luminy Ciml | Pekowska A.,French National Center for Scientific Research | Pekowska A.,French Institute of Health and Medical Research | Pekowska A.,Aix - Marseille University | And 35 more authors.
EMBO Journal | Year: 2011

Combinations of post-translational histone modifications shape the chromatin landscape during cell development in eukaryotes. However, little is known about the modifications exactly delineating functionally engaged regulatory elements. For example, although histone H3 lysine 4 mono-methylation (H3K4me1) indicates the presence of transcriptional gene enhancers, it does not provide clearcut information about their actual position and stage-specific activity. Histone marks were, therefore, studied here at genomic loci differentially expressed in early stages of T-lymphocyte development. The concomitant presence of the three H3K4 methylation states (H3K4me1/2/3) was found to clearly reflect the activity of bona fide T-cell gene enhancers. Globally, gain or loss of H3K4me2/3 at distal genomic regions correlated with, respectively, the induction or the repression of associated genes during T-cell development. In the Tcrb gene enhancer, the H3K4me3-to-H3K4me1 ratio decreases with the enhancer's strength. Lastly, enhancer association of RNA-polymerase II (Pol II) correlated with the presence of H3K4me3 and Pol II accumulation resulted in local increase of H3K4me3. Our results suggest the existence of functional links between Pol II occupancy, H3K4me3 enrichment and enhancer activity. © 2011 European Molecular Biology Organization | All Rights Reserved.

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